While you have groups that make up various bases with boxes, you do not have actual 'base' objects.

Include / replace boxes with base objects in order for bzfs to recognize your bases in CTF mode. Base map syntax can be found in the docs and in the wiki at http://wiki.bzflag.org/Base. Let us know if you have any other problems.

(I see I was a tad too late...Usually the forums say something if someone posts something new...)